The whole point is that I DO want Calibre to manage the devices, but only EPUBs and PDFs, and I can't tell Calibre what I want until it has already scanned all my CBR/CBZ and assorted other files. It seems nuts that Calibre Companion has a "scan on connect" toggle but Calibre itself does not.

Regardless, my wireless network seems faster than MTP anyway, so I'll probably just continue doing everything wirelessly. It might be worthwhile to disable MTP in Calibre just to avoid accidents.